So, right now, the script has it at port 8080, and that doesn't find the library at all. In the application, I got it working on 9090. Strange thing is, if I hit the "start server" button, it tells me that 9090 is unavailable - even though it's working now.

How many WEB servers are you running on that machine?

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I'm also trying to figure out why everything goes to poop when I reboot the machine. That is not optimal. Is there any error report I can run for you all to help analyze it?

Sounds like you have a shell script that is starting up multiple services and there is a race. (if you are starting from a Script. Don't have the Preference auto start Calibre WEB service.

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But, let me stress: This does not affect my feelings on the program. It's still the best book-management software I've used, and well worth it for this first instance of hassle. Thanks for all of your hard work in creating/maintaining it!

This is the first report of this nature I have seen (there have been others that are different ) in the year+ I have beenhaunting this board. This is a User specific issue.
BTW I have no problem with my Natty Desktop version: Calibre Server starts when I launch Calibre.